# Bio.Phylo.PAML.yn00 module

Classes for the support of yn00.

Yang and Nielsen 2000, estimating synonymous and nonsynonymous substitution rates in pairwise comparison of protein-coding DNA sequences.

exception Bio.Phylo.PAML.yn00.Yn00Error

  Bases: `OSError`

  yn00 failed. Run with verbose=True to view yn00’s error message.

  __firstlineno__ = 20
  __static_attributes__ = ()

class Bio.Phylo.PAML.yn00.Yn00(alignment=None, working_dir=None, out_file=None)

  Bases: `Paml`

  An interface to yn00, part of the PAML package.

  __init__(alignment=None, working_dir=None, out_file=None)

    Initialize the Yn00 instance.

    The user may optionally pass in strings specifying the locations of the input alignment, the working directory and the final output file.

  write_ctl_file()

    Dynamically build a yn00 control file from the options.

    The control file is written to the location specified by the ctl_file property of the yn00 class.

  read_ctl_file(ctl_file)

    Parse a control file and load the options into the yn00 instance.

  run(ctl_file=None, verbose=False, command='yn00', parse=True)

    Run yn00 using the current configuration.

    If parse is True then read and return the result, otherwise return None.

  __annotations__ = {}
  __firstlineno__ = 24
  __static_attributes__ = ('_options', 'alignment', 'ctl_file', 'out_file')

Bio.Phylo.PAML.yn00.read(results_file)

  Parse a yn00 results file.

Biopython v: 1.85

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